Using modified .CDF files in Genespring 9 / 10.

Change the array name in the header of the RNA .CEL files
(must be converted to version 3 and edited in Notepad or Wordpad). The new name must be identical to the custom technology that you have just made e.g. change ATH1-12501.1sq or HG-U133_Plus_2.1sq to xspecies_1.1sq

Create a new experiment using the modified .CEL files

Using modified .CDF files in Genespring 11.5.

Annotations>create technology>Affymetrix Expression

mammoth_100.cdf produces Affymetrix.GeneChip.mammoth_100

Edit your v3 .cels on the DatHeader= line (replace xxx.1sq with mammoth_100.1sq)

Create new project> create new experiment> [Affymetrix expression]
Select technology > Affymetrix.GeneChip.hamster_100
Choose the edited cel v3's
You will get a message that [ probes matched = xxxxx ]
Which should be the same as detailed in your CDF: NumberOfUnits=xxxxx